Glossary
A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z
The world of bioimaging and research data management is full of technical terms, abbreviations, and standards that can sometimes be difficult to navigate. This glossary is designed to help by providing clear and accessible explanations of commonly used concepts.
Whether you’re a researcher, data steward, facility staff member, student, or simply curious about bioimaging data, we hope this resource helps you better understand the terminology and practices that support FAIR, reusable, and high-quality research data.
A
AI
Artificial Intelligence; refers to computer systems designed to perform tasks that normally require human intelligence, such as recognizing patterns, interpreting images, understanding language, or making predictions.
Annotation
Additional information attached to data or images, such as labels, descriptions, regions of interest, or biological interpretations.
API
Application Programming Interface; A set of rules that allows software tools and services to communicate and exchange data automatically.
B
BAND
Bioimage ANalysis Desktop; a virtual analysis environment for bioimaging data that can be accessed through a web browser. It provides ready-to-use image analysis tools, high-performance computing resources, and optional GPU acceleration for computationally demanding workflows.
Base4NFDI
A joint initiative across all German NFDI consortia aiming to develop, scale, and provide foundational basic RDM services (e.g., Identity and Access Management, PID services) for the entire German research landscape.
Bio-Formats
An open-source tool that allows many microscopy file formats to be opened and used across different software applications. It helps make image data and metadata more accessible by translating proprietary formats into standardised, interoperable formats.
Bioimage Data
Digital image data generated from biological experiments using microscopy or other imaging technologies.
Block Storage
A data storage system that stores information in fixed-size blocks and provides raw storage that can be organised by a file system. It is commonly used for high-performance applications such as databases and virtual machines. Cloud environments usually use object storage.
C
CC
Creative Commons; A widely used system of open licences that helps researchers define how others can reuse datasets, images, publications, or other materials.
CPU
Central Processing Unit; the main processor of a computer that performs general-purpose calculations and controls program execution.
D
Data Curation
The process of organizing, documenting, improving, and maintaining data to ensure quality and reuse.
Data Spaces
Socio-technical frameworks and architectures (highly promoted in EU data strategies like Gaia-X) enabling trustworthy data sharing between distinct entities based on common governance rules.
Data Steward
A person who supports researchers in managing, documenting, sharing, and preserving research data according to good scientific practice and FAIR principles.
Dependencies
Software components, libraries, or packages that a program needs in order to run correctly. If a required dependency is missing or has a different version than expected, the software may not work as intended.
DMP
Data Management Plan; A document describing how research data will be collected, organized, stored, shared, and preserved during and after a project
DMPCommonStandard
An application profile (e.g., RDA DMP Common Standard) that makes Data Management Plans machine-actionable, allowing systems to automatically exchange and parse DMP information.
Docker
An open platform for packaging applications and their dependencies into portable containers. Docker helps ensure that software runs consistently across different computers, servers, and cloud environments, supporting reproducible research and computational workflows.
DOI
Digital Object Identifier; A persistent identifier used to uniquely identify digital objects such as datasets, publications, or software.
E
ELN
Electronic Lab Notebook; A digital software platform used by researchers to document experiments, protocols, and raw data acquisitions, serving as the first step in the RDM lifecycle.
EOSC
European Open Science Cloud; A European Commission initiative providing a virtual environment with open and seamless services for storage, management, analysis, and reuse of research data across borders.
F
FAIR Principles
Guidelines stating that research data should be Findable, Accessible, Interoperable, and Reusable.
FDO
FAIR Digital Object; A conceptual and technical anchor that bundles data, metadata, and persistent identifiers into an actionable unit that machines can reliably find, access, and interpret.
File Format
A standard way of structuring and storing digital data, such as TIFF, PNG, or OME-Zarr.
G
GitHub
An online platform for hosting, sharing, and collaborating on software code, documentation, and version-controlled projects.
GPU
Graphics Processing Unit; a specialized processor designed for parallel computations, widely used for image processing, machine learning, and AI applications.
GUI
Graphical User Interface; a visual interface that allows users to interact with software through windows, buttons, menus, and other graphical elements instead of command-line instructions.
H
Help Desk
A support service that provides assistance, guidance, and answers to user questions related to tools, data management, or infrastructure.
I
Interoperability
The ability of different software systems, formats, and datasets to work together and exchange information effectively.
J
Jupyter Notebook
An interactive, web-based computing environment that allows users to write and execute code, combine it with explanatory text, and display visualisations and results in a single document. It is widely used for data analysis, scientific computing, and reproducible research workflows.
K
Knowledge Graph
A programmatic representation of a network of real-world entities and their interrelations, increasingly used by European repositories to link metadata, creators, funding, and publications semantically.
L
LLM
Large Language Model; an AI model trained on large amounts of text data to understand and generate human language.
M
Machine-Readable
Structured in a way that allows computers to process and interpret information automatically.
Metadata
A structured framework or blueprint that defines the rules, attributes, and relationships used to comprehensively document specific data types.
N
NFDI
Nationale ForschungsDatenInfrastruktur (National ResearchDataInfrastructure); Germany’s National Research Data Infrastructure, a nationwide initiative to systematically manage scientific and research data across various consortia.
NGFF
Next-Generation File Formats; modern file format specifications designed for scalable, cloud-compatible, and interoperable storage of large multidimensional imaging datasets.
O
Object Storage
A scalable data storage architecture that stores data as objects, each containing the data itself, metadata, and a unique identifier, commonly used in cloud environments. Alternative to traditional block storage.
OME
Open Microscopy Environment; An open community-driven project developing standards and tools for biological imaging data.
OMERO
An open-source platform for managing, visualising, sharing, and analysing microscopy and bioimaging data.
OME-NGFF
OME Next-Generation File Formats; A collection of standards developed by OME for modern bioimaging data storage. OME-Zarr is one implementation of the OME-NGFF.
OME-Zarr
An open, cloud-compatible bioimaging file format designed for storing large multidimensional image datasets efficiently.
Ontology
A structured and standardized representation of concepts and their relationships within a scientific domain.
Open Data
Research data that are freely available for access, reuse, and redistribution.
Open Science
An approach to research that promotes transparency, accessibility, collaboration, and sharing of scientific knowledge.
ORCID
Open Researcher and Contributor ID; A persistent digital identifier that uniquely distinguishes researchers and connects them with their publications, datasets, software, and other research outputs.
P
PID
Persistent Identifier; A long-lasting reference assigned to a digital object, person, or organization to ensure reliable identification.
Proprietary File Format
A file format developed by a specific microscope manufacturer or software provider. Accessing the data may require specialized software, which is why tools such as Bio-Formats are important for interoperability and data reuse.
Provenance
Information documenting the origin, history, and processing of data.
Q
QUAREP-LiMi
An international community initiative that develops standards, best practices, and tools to improve the quality, reproducibility, and standardization of light microscopy and its data.
R
Raw Data
Original data generated directly by an instrument before processing or analysis.
RDM
Research Data Management; The organization, documentation, storage, sharing, and preservation of research data throughout its lifecycle.
REMBI
Recommended Metadata for Biological Images; A community guideline defining the minimum metadata needed to describe and share bioimaging experiments in a consistent and reusable way.
Repository
A platform or infrastructure for storing, preserving, and sharing research data.
Reproducibility
The ability to obtain consistent results using the same data, methods, and analysis workflow.
RFC
Request for Comments; a formal document used to propose, describe, and standardize protocols, formats, or best practices in technical communities.
RO-Crate
A machine-readable package format for describing and sharing research data, metadata, workflows, and associated resources.
ROR
Research Organization Registry; A community-led registry of persistent identifiers for research organizations, critical for institutional attribution in RDM infrastructure.
S
Semantic Annotation
The use of standardized terms or ontologies to add structured meaning to data and metadata.
Spatial omics
Refers to technologies that measure molecular information, such as genes, proteins, or metabolites, while preserving the spatial context within tissues or cells.
Standard
An agreed specification or guideline that ensures consistency and interoperability across tools and datasets.
S3
Simple Storage Service; a widely used cloud object storage protocol and service model that enables scalable storage and retrieval of large datasets.
T
U
URI
Uniform Resource Identifier; a standardized identifier used to uniquely identify a resource on the internet, such as a dataset, file, or web service.
URL
Uniform Resource Locator; is a type of URI that not only identifies a resource but also provides its location and how to access it (e.g. via HTTPS).
V
Version Control
A system for tracking and managing changes to files, datasets, or software over time.
Vitessce
An open-source web-based visualization platform for exploring and integrating spatial omics and imaging datasets interactively.
W
X
Y
Z
Zenodo
An open-access research repository that allows researchers to upload, share, preserve, and cite datasets, software, publications, and other research outputs. Explore our Zenodo community!